Contacts of the strand formed by residues 136 - 140 (chain A) in PDB entry 1D4O
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A VAL* 3.5 7.9 - - + +
103A VAL* 3.7 29.4 - - + -
130A VAL* 3.3 36.8 - - + +
131A TRP* 4.2 8.7 - - - -
133A SER* 3.4 8.7 - - - +
135A GLN* 1.3 79.4 + - - +
137A ILE* 1.3 64.9 + - - +
138A VAL* 4.0 15.7 - - + -
154A ILE* 4.7 2.7 - - + -
159A ASN* 2.8 17.6 + - - +
160A THR* 3.9 13.0 - - - +
161A ALA 2.9 25.3 + - - -
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Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 4.0 7.4 - - + -
15A ALA* 4.0 25.8 - - + +
18A MET* 3.7 32.5 - - + -
19A ILE* 5.4 0.2 - - + -
100A LEU* 4.0 12.8 - - + -
101A VAL 2.9 6.5 + - - -
102A LEU* 3.7 23.5 - - + -
103A VAL* 2.8 28.2 + - - +
136A VAL* 1.3 77.9 - - - +
138A VAL* 1.3 64.1 + - - +
139A MET* 4.0 8.5 + - + +
161A ALA* 3.3 7.0 - - + +
163A LEU* 3.6 35.0 - - + -
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Residues in contact with VAL 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 3.6 21.3 - - + -
106A ALA 4.8 1.3 - - - +
136A VAL* 4.0 12.6 - - + -
137A ILE* 1.3 74.4 - - - +
139A MET* 1.3 63.1 + - - +
140A LYS* 3.6 31.1 + - + -
154A ILE* 4.1 14.6 - - + -
155A PHE* 4.0 9.9 - - + -
160A THR* 3.9 22.7 - - + -
161A ALA 2.9 8.1 + - - -
162A MET* 3.6 22.6 - - + +
163A LEU 2.9 28.3 + - - +
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Residues in contact with MET 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ALA* 6.2 0.2 - - + -
45A LEU* 6.2 0.7 - - + -
102A LEU* 4.1 28.0 - - + -
103A VAL 2.8 15.3 + - - +
104A ILE* 3.9 36.0 - - + +
105A GLY* 3.0 25.6 + - - -
137A ILE* 4.4 5.2 - - + +
138A VAL* 1.3 74.0 - - - +
140A LYS* 1.3 61.6 + - - +
163A LEU* 3.5 27.4 - - + +
165A GLY 4.9 2.0 - - - +
167A ALA* 5.2 5.5 - - + +
170A THR* 3.8 23.8 - - + +
171A CYS* 4.0 14.1 - - - -
174A LEU* 3.6 23.3 - - + -
201A NAP 4.4 2.9 + - - -
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Residues in contact with LYS 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A GLY* 5.2 1.8 - - - -
106A ALA 4.9 4.9 - - - +
107A ASN* 3.8 7.0 - - - +
138A VAL* 3.6 25.2 + - + -
139A MET* 1.3 75.5 - - - +
141A ARG* 1.3 61.4 + - - +
142A SER 2.8 22.7 + - - +
143A LEU 3.9 1.4 - - - -
144A GLY 2.9 28.9 + - - +
155A PHE* 3.7 19.3 - - + -
162A MET* 4.1 6.7 - - + -
163A LEU 3.9 1.6 + - - -
164A LEU* 3.3 8.5 - - - +
165A GLY 2.9 23.7 + - - -
201A NAP 2.8 64.2 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il